Contacts of the helix formed by residues 298 - 326 (chain C) in PDB entry 6FF7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 298 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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811A THR* 6.4 1.6 - - - -
814A VAL* 4.8 18.2 - - + -
294C ALA 2.8 13.7 + - - +
295C ASP* 3.6 6.5 - - - +
296C ARG 3.4 0.2 - - - -
297C LYS* 1.3 80.6 - - - +
299C ARG* 1.3 56.7 + - - +
300C GLU 3.6 1.3 - - - -
301C ALA* 3.0 8.8 + - - +
302C VAL* 2.7 37.4 + - + +
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Residues in contact with ARG 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ASP* 2.7 22.6 + - + +
296C ARG* 4.7 2.7 - - - -
298C ALA* 1.3 71.2 - - - +
300C GLU* 1.3 54.2 + - - +
302C VAL* 3.0 9.1 + - - +
303C GLU* 2.7 35.9 + - - +
446u MET* 5.9 0.7 - - - +
447u GLN* 5.4 13.7 - - + -
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ARG* 5.4 8.1 + - - +
299C ARG* 1.3 76.4 - - - +
301C ALA* 1.3 53.3 + - - +
303C GLU* 3.0 9.4 + - - +
304C MET* 2.5 38.2 + - - +
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Residues in contact with ALA 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LYS 4.3 11.6 - - - +
298C ALA* 3.0 13.7 + - - +
300C GLU* 1.3 78.0 - - - +
302C VAL* 1.3 61.4 + - - +
304C MET* 3.0 10.3 + - - +
305C ARG* 2.9 22.0 + - - +
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Residues in contact with VAL 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A VAL* 6.1 4.5 - - + +
818A GLU* 5.3 13.0 - - + -
298C ALA* 2.7 18.1 + - + +
299C ARG* 3.4 9.4 - - - +
301C ALA* 1.3 70.7 - - - +
303C GLU* 1.3 62.4 + - - +
305C ARG* 3.0 11.6 + - - +
306C ALA* 3.0 20.4 + - - +
445u HIS 5.6 2.0 - - - +
446u MET* 5.1 18.6 - - + +
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Residues in contact with GLU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ARG 2.7 17.0 + - - +
300C GLU* 3.3 13.0 - - - +
302C VAL* 1.3 71.8 - - - +
304C MET* 1.3 63.6 + - - +
306C ALA* 3.0 12.1 + - - +
307C GLN* 3.0 22.2 + - - +
446u MET* 5.2 10.9 - - + +
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Residues in contact with MET 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C GLU 2.5 22.3 + - - +
301C ALA* 3.0 15.7 + - - +
303C GLU* 1.3 71.6 - - - +
305C ARG* 1.3 62.6 + - - +
307C GLN* 3.1 9.5 + - - +
308C VAL* 2.9 23.6 + - - +
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Residues in contact with ARG 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A GLU* 6.3 3.4 - - + -
301C ALA 2.9 11.2 + - - +
302C VAL* 3.0 12.8 + - - +
304C MET* 1.3 73.9 - - - +
306C ALA* 1.3 57.4 + - - +
308C VAL* 3.1 6.6 + - - +
309C GLU* 2.8 32.2 + - - +
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Residues in contact with ALA 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C VAL 3.0 11.8 + - - +
303C GLU* 3.2 14.8 - - - +
305C ARG* 1.3 73.4 - - - +
307C GLN* 1.3 63.1 + - - +
309C GLU* 3.1 8.2 + - - +
310C ARG* 3.0 21.9 + - - +
444u PHE* 6.2 4.3 - - + -
445u HIS 5.8 3.4 - - - +
446u MET* 5.7 6.7 - - + -
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Residues in contact with GLN 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLU 3.0 11.3 + - - +
304C MET* 3.1 10.5 + - - +
306C ALA* 1.3 74.7 - - - +
308C VAL* 1.3 52.7 + - - +
310C ARG* 3.1 9.9 + - - +
311C LYS* 2.7 34.3 + - - +
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Residues in contact with VAL 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C MET 2.9 14.9 + - - +
305C ARG* 3.1 6.0 + - - +
307C GLN* 1.3 76.0 - - - +
309C GLU* 1.3 57.4 + - - +
311C LYS* 3.1 12.2 + - + +
312C MET* 2.8 28.8 + - - +
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Residues in contact with GLU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ARG 2.8 16.6 + - - +
306C ALA* 3.5 7.2 - - - +
308C VAL* 1.3 76.7 - - - +
310C ARG* 1.3 57.1 + - - +
312C MET* 3.1 10.0 + - - +
313C ALA* 2.8 25.7 + - - +
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Residues in contact with ARG 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ALA 3.0 12.3 + - - +
307C GLN* 3.1 10.5 + - - +
309C GLU* 1.3 76.0 - - - +
311C LYS* 1.3 51.5 + - - +
313C ALA* 3.0 12.2 + - + +
314C GLN* 2.7 34.3 + - - +
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Residues in contact with LYS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C GLN 2.7 17.0 + - - +
308C VAL* 3.1 16.1 + - + +
310C ARG* 1.3 72.2 - - - +
312C MET* 1.3 56.8 + - - +
314C GLN* 3.0 10.7 + - - +
315C LYS* 3.0 26.2 + - - +
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Residues in contact with MET 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C VAL 2.8 12.6 + - - +
309C GLU* 3.5 10.1 - - - +
311C LYS* 1.3 72.1 - - - +
313C ALA* 1.3 55.2 + - - +
315C LYS* 3.0 9.1 + - - +
316C GLU* 2.8 38.6 + - + +
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Residues in contact with ALA 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C GLU 2.8 12.9 + - - +
310C ARG* 3.0 18.1 + - + +
312C MET* 1.3 76.1 - - - +
314C GLN* 1.3 55.3 + - - +
316C GLU* 3.0 19.6 + - - +
317C LYS* 3.2 19.2 + - + +
318C GLU* 4.0 3.5 + - - +
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Residues in contact with GLN 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ARG 2.7 15.6 + - - +
311C LYS* 3.0 12.1 + - - +
313C ALA* 1.3 72.0 - - - +
315C LYS* 1.3 58.6 + - - +
318C GLU* 4.2 17.1 - - - +
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C LYS 3.0 11.4 + - - +
312C MET* 3.0 10.7 + - - +
314C GLN* 1.3 80.6 - - - +
316C GLU* 1.3 62.4 + - - +
319C LYS* 3.4 19.6 - - - +
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Residues in contact with GLU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C MET 2.8 16.6 + - - +
313C ALA* 3.0 2.7 + - - +
315C LYS* 1.3 79.4 - - - +
317C LYS* 1.3 62.8 + - + +
318C GLU 3.4 0.2 - - - -
319C LYS* 3.0 9.5 + - - +
320C HIS* 3.0 25.2 + - - +
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Residues in contact with LYS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ALA* 3.2 12.1 + - + +
316C GLU* 1.3 79.1 - - + +
318C GLU* 1.3 58.0 + - - +
320C HIS* 3.0 13.1 + - - +
321C GLU* 2.9 24.9 + - - +
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ALA 4.0 3.2 + - - +
314C GLN* 4.2 21.8 - - - +
316C GLU 3.4 0.4 - - - -
317C LYS* 1.3 77.9 - - - +
319C LYS* 1.3 56.9 + - - +
321C GLU* 2.9 29.1 + - - +
322C GLU* 3.5 3.8 + - - +
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Residues in contact with LYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C LYS 3.4 17.9 + - - +
316C GLU* 3.0 12.3 + - - +
318C GLU* 1.3 76.8 - - - +
320C HIS* 1.3 57.4 + - - +
322C GLU* 3.0 24.1 + - - +
323C LYS* 3.3 8.4 + - - +
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Residues in contact with HIS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C GLU 3.0 10.6 + - - +
317C LYS* 3.0 15.1 + - - +
319C LYS* 1.3 72.7 - - - +
321C GLU* 1.3 54.3 + - - +
323C LYS* 3.0 16.2 + - + +
324C LEU* 2.7 33.9 + - - +
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Residues in contact with GLU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C LYS 2.9 9.7 + - - +
318C GLU* 2.9 21.1 + - - +
320C HIS* 1.3 76.3 - - - +
322C GLU* 1.3 48.2 + - - +
324C LEU* 3.0 10.2 + - - +
325C ARG* 2.6 36.5 + - - +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C GLU 3.5 3.5 + - - +
319C LYS* 3.0 13.1 + - - +
321C GLU* 1.3 76.8 - - - +
323C LYS* 1.3 58.4 + - - +
325C ARG* 3.0 10.1 + - + +
326C GLU* 2.9 35.1 + - + +
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Residues in contact with LYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LYS 3.3 3.9 + - - +
320C HIS* 3.0 24.3 + - + +
322C GLU* 1.3 76.1 - - - +
324C LEU* 1.3 55.5 + - - +
326C GLU 5.1 1.5 - - - +
327C MET* 5.0 9.4 + - - +
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C HIS 2.7 13.6 + - - +
321C GLU* 3.0 11.9 + - - +
323C LYS* 1.3 75.6 - - - +
325C ARG* 1.3 63.6 + - - +
327C MET* 4.7 5.8 + - - +
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Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C GLU 2.6 20.0 + - - +
322C GLU* 3.0 10.4 + - + +
324C LEU* 1.3 78.6 - - - +
326C GLU* 1.3 61.2 + - + +
327C MET* 3.0 8.8 + - - +
331C ALA* 4.4 8.7 - - - +
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C GLU* 2.9 20.9 + - + +
323C LYS* 5.1 2.6 - - - +
325C ARG* 1.3 71.2 - - + +
327C MET* 1.3 65.0 + - - +
328C ALA* 3.3 5.0 + - - +
331C ALA* 5.1 3.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il